MolNFT v1 · #55032 · protein + DNA
Atomic model of the DNA-bound methylase complex from the type I restriction-modification enzyme ecoki (M2S1). based on fitting into EM MAP 1534.
2Y7H · Type-1 restriction enzyme ecoki specificity protein: “Atomic model of the DNA-bound methylase complex from the type I restriction-modification enzyme ecoki (M2S1).…”. Electron microscopy, 1 ligand (SAM), 20 pockets (best…
- PDB
- 2Y7H
- Type
- protein + DNA
- Length
- 1,562 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-1 restriction enzyme ecoki specificity protein; Type I restriction enzyme ecoki M…
- EC
- 3.1.21.3, 2.1.1.72
- UniProt
- P05719, P08957
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-1 restriction enzyme ecoki specificity protein (EC 3.1.21.3) | protein | 464 | 44% helix, 16% strand | P05719 |
| B, C | Type I restriction enzyme ecoki M protein (EC 3.1.21.3, 2.1.1.72) | protein | 529 | 47% helix, 12% strand | P08957 |
| D | 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3' | dna | 20 | — | — |
| E | 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3' | dna | 20 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.87 | 0.89 | 142 | SAM |
| 2 | 200 | 0.82 | 0.95 | 53 | empty |
| 3 | 1132 | 0.81 | 0.82 | 117 | empty |
| 4 | 88 | 0.73 | 0.95 | 28 | empty |
| 5 | 256 | 0.71 | 0.86 | 33 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1330 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1178 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 1040 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–D · 1037 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–C · 980 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2Y7H · Atomic model of the DNA-bound methylase complex from the Type I restriction-modification… · the same entry in another collection · chain A against A, TM-score 1.00
- P08957 · AlphaFold monomer V2.0 prediction for type I restriction enzyme ecoki M protein (P08957) · a predicted model of the same protein · chain C against A, TM-score 0.82
- P05719 · AlphaFold monomer V2.0 prediction for type-1 restriction enzyme ecoki specificity protein… · a predicted model of the same protein · chain A against A, TM-score 0.69
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05719
- Every structure of UniProt P08957
- Elsewhere: RCSB PDB 2Y7H · PDBe 2Y7H · UniProt P05719 · UniProt P08957
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